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Title: Determination and Comparison of the Baseline Proteomes of the Versatile Microbe Rhodopseudomonas palustris under its Major Metabolic States

Abstract

Rhodopseudomonas palustris is a purple nonsulfur anoxygenic phototrophic bacterium that is ubiquitous in soil and water. R. palustris is metabolically versatile with respect to energy generation and carbon and nitrogen metabolism. We have characterized and compared the baseline proteome of a R. palustris wild-type strain grown under six metabolic conditions. The methodology for proteome analysis involved protein fractionation by centrifugation, subsequent digestion with trypsin, and analysis of peptides by liquid chromatography coupled with tandem mass spectrometry. Using these methods, we identified 1664 proteins out of 4836 predicted proteins with conservative filtering constraints. A total of 107 novel hypothetical proteins and 218 conserved hypothetical proteins were detected. Qualitative analyses revealed over 311 proteins exhibiting marked differences between conditions, many of these being hypothetical or conserved hypothetical proteins showing strong correlations with different metabolic modes. For example, five proteins encoded by genes from a novel operon appeared only after anaerobic growth with no evidence of these proteins in extracts of aerobically grown cells. Proteins known to be associated with specialized growth states such as nitrogen fixation, photoautotrophic, or growth on benzoate, were observed to be up-regulated under those states.

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [2];  [1];  [1];  [3];  [4];  [5];  [6];  [1]
  1. ORNL
  2. {Greg} B [ORNL
  3. University of British Columbia, Vancouver
  4. University of Washington, Seattle
  5. Ohio State University
  6. {Bob} L [ORNL
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
978060
DOE Contract Number:
DE-AC05-00OR22725
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Proteome Research; Journal Volume: 5; Journal Issue: 2
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; 99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; CARBON; CENTRIFUGATION; CHROMATOGRAPHY; DIGESTION; FRACTIONATION; GENES; MASS SPECTROSCOPY; METABOLISM; NITROGEN; NITROGEN FIXATION; PEPTIDES; PROTEINS; RHODOPSEUDOMONAS; SOILS; STRAINS; TRYPSIN; WATER

Citation Formats

Verberkmoes, Nathan C, Shah, Manesh B, Lankford, Patricia K, Pelletier, Dale A, Strader, Michael B, Tabb, Dave L, McDonald, W Hayes, Barton, John W, Hurst, Gregory, Hauser, Loren John, Davison, Brian H, Beatty, Thomas, Harwood, Caroline S, Tabita, F Robert, Hettich, Robert, and Larimer, Frank W. Determination and Comparison of the Baseline Proteomes of the Versatile Microbe Rhodopseudomonas palustris under its Major Metabolic States. United States: N. p., 2006. Web. doi:10.1021/pr0503230.
Verberkmoes, Nathan C, Shah, Manesh B, Lankford, Patricia K, Pelletier, Dale A, Strader, Michael B, Tabb, Dave L, McDonald, W Hayes, Barton, John W, Hurst, Gregory, Hauser, Loren John, Davison, Brian H, Beatty, Thomas, Harwood, Caroline S, Tabita, F Robert, Hettich, Robert, & Larimer, Frank W. Determination and Comparison of the Baseline Proteomes of the Versatile Microbe Rhodopseudomonas palustris under its Major Metabolic States. United States. doi:10.1021/pr0503230.
Verberkmoes, Nathan C, Shah, Manesh B, Lankford, Patricia K, Pelletier, Dale A, Strader, Michael B, Tabb, Dave L, McDonald, W Hayes, Barton, John W, Hurst, Gregory, Hauser, Loren John, Davison, Brian H, Beatty, Thomas, Harwood, Caroline S, Tabita, F Robert, Hettich, Robert, and Larimer, Frank W. Sun . "Determination and Comparison of the Baseline Proteomes of the Versatile Microbe Rhodopseudomonas palustris under its Major Metabolic States". United States. doi:10.1021/pr0503230.
@article{osti_978060,
title = {Determination and Comparison of the Baseline Proteomes of the Versatile Microbe Rhodopseudomonas palustris under its Major Metabolic States},
author = {Verberkmoes, Nathan C and Shah, Manesh B and Lankford, Patricia K and Pelletier, Dale A and Strader, Michael B and Tabb, Dave L and McDonald, W Hayes and Barton, John W and Hurst, Gregory and Hauser, Loren John and Davison, Brian H and Beatty, Thomas and Harwood, Caroline S and Tabita, F Robert and Hettich, Robert and Larimer, Frank W},
abstractNote = {Rhodopseudomonas palustris is a purple nonsulfur anoxygenic phototrophic bacterium that is ubiquitous in soil and water. R. palustris is metabolically versatile with respect to energy generation and carbon and nitrogen metabolism. We have characterized and compared the baseline proteome of a R. palustris wild-type strain grown under six metabolic conditions. The methodology for proteome analysis involved protein fractionation by centrifugation, subsequent digestion with trypsin, and analysis of peptides by liquid chromatography coupled with tandem mass spectrometry. Using these methods, we identified 1664 proteins out of 4836 predicted proteins with conservative filtering constraints. A total of 107 novel hypothetical proteins and 218 conserved hypothetical proteins were detected. Qualitative analyses revealed over 311 proteins exhibiting marked differences between conditions, many of these being hypothetical or conserved hypothetical proteins showing strong correlations with different metabolic modes. For example, five proteins encoded by genes from a novel operon appeared only after anaerobic growth with no evidence of these proteins in extracts of aerobically grown cells. Proteins known to be associated with specialized growth states such as nitrogen fixation, photoautotrophic, or growth on benzoate, were observed to be up-regulated under those states.},
doi = {10.1021/pr0503230},
journal = {Journal of Proteome Research},
number = 2,
volume = 5,
place = {United States},
year = {Sun Jan 01 00:00:00 EST 2006},
month = {Sun Jan 01 00:00:00 EST 2006}
}